replace PyCogent calls with BiPy calls

biocore / qiime

Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.

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replace PyCogent calls with BiPy calls #1369

Closed gregcaporaso closed 10 years ago

gregcaporaso commented 10 years ago

Add to this check list as you identify code that is ready to be changed.

[ ] calls to cogent.DNA.rc() should be replaced with calls to bipy.core.sequence.DNA().rc()``
[ ] calls to cogent.parse.fasta.MinimalFastaParser should be replaced with calls to bipy.parse.fasta.MinimalFastaParser (and we may want to change that name to something like FastaRecords as it's a generator of (seq_id, seq) pairs.

wasade commented 10 years ago

I'm concerned about bipy.core.sequence.DNA().rc(), shouldn't this be a classmethod?

gregcaporaso commented 10 years ago

yes, probably. can you add an issue to the bipy issue tracker.

On Fri, Jan 31, 2014 at 8:48 AM, Daniel McDonald notifications@github.comwrote:

I'm concerned about bipy.core.sequence.DNA().rc(), shouldn't this be a classmethod?

Reply to this email directly or view it on GitHubhttps://github.com/qiime/qiime/issues/1369#issuecomment-33804975 .

wasade commented 10 years ago

Done, see biocore/bipy#73

jairideout commented 10 years ago

[x] cogent.util.misc.app_path should be replaced with bipy.util.which (this depends on https://github.com/biocore/bipy/issues/45 being completed first)

jairideout commented 10 years ago

[ ] qiime.util.DistanceMatrix should be replaced with bipy.core.distance.DistanceMatrix (see #829). Also, the usage of (sample_ids, data) distance matrix tuple should be replaced with the new DistanceMatrix class.

gregcaporaso commented 10 years ago

this has been split into individual issues, many of which have already been taken care of.